Passing the study plan

State doctoral examination and defence of the dissertation are held in English language.

STATE DOCTORAL EXAMINATION (SDE)
is usually taken after completing the fourth semester of study and it verifies:
i) deep knowledge of details within the context of the particular doctoral project,
ii) professional orientation – the student demonstrates his/her good understanding of issues related to the Hard-skills courses completed, in the contemporary methodologies and technologies, and
iii) broad knowledge within the Life Sciences Programme.

The Chair of the Doctoral Board together with the Supervisor determine three scientific areas. The student is acquainted with these areas no later than two weeks after submitting the application for SDE. He/she will choose one of them, for which he/she will prepare and present a professional presentation lasting 10 minutes to the Evaluation Committee during the SDE. The presentation is followed by a detail discussion of the three assigned scientific areas. The basic scientific areas are summarized in the syllabus of the study programme.

DISSERTATION (DOCTORAL THESIS)
The dissertation presents the results of the creative activity performed by the candidate during the study. It must contain the original results that were published or accepted for publication. The work should be sufficiently detailed to allow the Evaluation Committee to assess the student's scientific, methodological, and critical thinking.
The dissertation can be elaborated in two various formats the selection of which must be approved by the Supervisor.

The preferred format of the dissertation is a set of papers with a comprehensive introduction and commentary. This type of dissertation is based on at least two publications, of which at least one must be a first-author. If this publication does not have an IF in Q1 in a given field of study, there should be two more co-authored publications with an IF in Q1 or Q2. Reviews may also be part of the work, but cannot be included in the limit of two publications. Only published articles or manuscripts accepted for publication with an acceptance letter may be included.

The thesis should contain i) an introduction, ii) the hypothesis and objectives of the project, iii) methodology (optional), iii) commentary on published contributions (unpublished work may be also included), iv) specification of the student’s own contribution on all results contained in the publications, v) a summary of the results and the way in which they disseminate knowledge in the field, vi) a discussion that provides context and comments on the results, vii) conclusion, viii) references.

The second format of the dissertation is a monograph with experimental results. It contains a complete description of the dissertation project and can be written as an extended version of the publication. The thesis should be sufficiently detailed to allow the Evaluation Committee to assess the student's scientific, methodological, and critical thinking (the maximum length should not exceed 120 pages).

The thesis is divided into i) introduction, ii) hypothesis and goals of the project, iii) methods, vi) results, v) discussion that provides context and comments on the results, vi) conclusion, vii) specification of the student’s own contribution to the work on all included results and links.

DEFENCE OF THE DISSERTATION
The defence takes the form of a 20-minute presentation of the results of the doctoral project, followed by a discussion clarifying the comments and questions of the opponents and other questions from the members of the Evaluation Committee.

In exceptional cases, it is possible to proceed with the defence in the form of Viva Voce (Anglo-Saxon method of defence). The form of defence in this way is significantly stringent (it is described in detail in the Self-Assessment Report of the Programme). The proposal for it is submitted by the Supervisor and discussed/approved by the Doctoral Board.

According to the Masaryk University Study and Examination Regulations, during the first year of study, each student compiles an Individual Study Plan (ISP) in cooperation with the Supervisor, which is recorded in the MU Information System (IS MU). The total expected load corresponds to about 60 ECTS credits per year (1 credit is about 25 hours, i.e. a total of 1500 hours of study and research duties per year). The ISP is approved by the Doctoral Board.
The plans for each semester are specified in the Term content, which is approved by the Supervisor, and the fulfillment of which is evaluated by the Supervisor at the end of each semester.
The student is also obliged, after discussion with the Supervisor and the Doctoral Board, to create an individual Thesis Advisory Committee (TAC) during the first semester of study, composed of at least three experts (including the Supervisor) in the field of their doctoral thesis. The task of the TAC is to help the student set up the ISP, monitor its implementation, and provide feedback on the course of study and scientific progress. The three planned meetings of this Advisory Committee serve as milestones for the study and a record is made of each, which informs the Doctoral Board about the student's progress and the phase of fulfilling the set goals in a suitable form and to an adequate extent.

The Individual Study Plan is based on the fulfillment of requirements covering three areas, whereas two of them are common for all students of the programme and the last one differs according to individual student’s specialization. The three areas are:
- Core subjects - about 65% of the study content
- Soft-skills courses – about 15% of the study content
- Hard-skills courses - about 20% of the study content

Core subjects make up about 65% of all duties and serve to deepen the student’s scientific research competencies. The student is obliged to complete all basic subjects to a prescribed extent. The largest part of about 50% represents experimental and other scientific activities on the research project, about 10% is active participation in scientific seminars, about 3% are activities related to data presentation, i.e. writing publications and active participation in conferences and about 2% of planned time represents a stay abroad.
The fulfillment of core subjects also takes into account the obligation of students to hold three TAC meetings during their studies, and the obligation to present their project within the PhD Conference in the third and fourth year of study.

Soft-skills courses make up about 15% of the total study content and serve to further develop students in areas that are indirectly related to their professional education, but which are necessary for their further career, especially in international, interdisciplinary and intersectoral contexts.
The students are obliged to complete at least three soft-skills courses during their study.
This type of courses also includes the subject Teaching Assistance, in which students gain pedagogical experience by participating in contact teaching or by leading Bachelor-degree or Master-degree students. The maximum extent is 150 hours of teaching throughout the study.

Hard-skills courses make up approximately 20% of the total study content. They aim to prepare the student professionally and are therefore selected specifically according to the needs of individual students. The student must complete at least four courses during the entire study.

In the combined form of study, which is offered to students completing the dissertation after the standard period of study, it is assumed that the subjects of all three specified areas have been already met, and only partial requirements are adjusted (e.g. attending periodic seminars).

A structural basis for the cross-talk between histones and RNA Polymerase II
ADAR2 RNA editing in CNS
Cracking the CTD code
Development of bioinformatics methods for data integration from various diagnostic types in clinical oncology
Developmental responses and adaptation to abiotic stress for seed production in rapeseed
Dynamics of the Structure Maintenance of Chromosome (SMC) complexes
Elucidation of novel therapy targets for B-cell malignancies
Characterization of cyclin-dependent kinases 12 and 11 (CDK12 and CDK11) in gene expression and tumorigenesis
Identification of RNA binding protein function and regulation patterns
Investigating the regulation of the RNA modifying enzyme ADAR1 and how it regulates other biological pathways and diseases
Microenvironmental interactions and non-coding RNAs in the biology of B cell leukemia
Regulation of protein-protein interactions
RNA as a drug target
Role of phosphorylated 14-3-3 proteins
Search for new regulators of intracellular trafficking in plants
Simultaneous gene transcription and translation in bacteria
Structural and time-resolved studies of phage replication in bacterial biofilm
Structural Biology of WNT Signalling
Structure, dynamics, and interactions of bacterial RNA polymerase subunits and sigma factors
Structure, function, and evolution of plant telomere components
Structure of parallel forms of nucleic acids studied by NMR spectroscopy and molecular modelling
Structure-functional study of proteins involved in host cell recognition
The role of protein-protein interactions in the dynamics of m6A RNA modification